Introduction
Data Source
Sample Data
Below are the metadata associated with each sample, as provided by LifeMine.
S000565
Feature Counts
The table below contains the normalized feature counts per locus ID for each sample.
S000565
Genes in Cluster
This is the clustergenes table as provided by LifeMine, which contains the genes and locus IDs from the cluster of interest.
S000565
Quality Control
Violin Plots
Let’s take a quick look at the distribution of counts for each sample.
Expressed genes
The following is a table of the number of expressed genes in each samples, giving a quantititive value to the quality of the expression data. Two thresholds for normalized gene expression were used here: 0.5 and 1.
S000565
ERCC controls
Shown here are some simple plots of ERCC concentrations after normalization.
S000565_WT_NA_1 vs. S000565_WT_NA_2
S000565_WT_NA_1 vs. S000565_S000631_PKS_KO_NA_1
S000565_WT_NA_1 vs. S000565_S000631_PKS_KO_NA_2
S000565_WT_NA_1 vs. S000565_TF_KI_NA_1
S000565_WT_NA_1 vs. S000565_TF_KI_NA_2
S000565_WT_NA_1 vs. S000565_S000631_TF_KI_NA_2
S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_NA_1
S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_NA_2
S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_NA_3
S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_NA_4
S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_NA_6
S000565_WT_NA_1 vs. S000565_WT_NA_1
S000565_WT_NA_1 vs. S000565_WT_NA_2
S000565_WT_NA_1 vs. S000565_S000631_PKS_KO_NA_1
S000565_WT_NA_1 vs. S000565_S000631_PKS_KO_NA_2
S000565_WT_NA_1 vs. S000565_TF_KI_NA_1
S000565_WT_NA_1 vs. S000565_TF_KI_NA_2
S000565_WT_NA_1 vs. S000565_S000631_TF_KI_NA_1
S000565_WT_NA_1 vs. S000565_S000631_TF_KI_NA_2
S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_NA_1
S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_NA_2
S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_NA_3
S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_NA_4
S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_NA_5
S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_NA_6
S000565_WT_NA_1 vs. S000565_WT_NA_1
S000565_WT_NA_1 vs. S000565_WT_NA_2
S000565_WT_NA_1 vs. S000565_S000631_PKS_KO_no41_NA_1
S000565_WT_NA_1 vs. S000565_S000631_PKS_KO_no41_NA_2
S000565_WT_NA_1 vs. S000565_TF_KI_no10_NA_1
S000565_WT_NA_1 vs. S000565_TF_KI_no10_NA_2
S000565_WT_NA_1 vs. S000565_S000631_TF_KI_no1_NA_1
S000565_WT_NA_1 vs. S000565_S000631_TF_KI_no1_NA_2
S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_no3_NA_1
S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_no3_NA_2
S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_no13_NA_1
S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_no13_NA_2
S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_no15_NA_1
S000565_WT_NA_1 vs. S000565_Etag_KI_TF_KI_no15_NA_2
Differential expression
Volcano plot
This volcano plot shows us a summary view of the differential expression results. Each point on the plot represents one gene in the experiment. Mouse over a point to see a pop-up view with details on the results for that gene. Interactive plots like this are computationally intensive, so we’re only showing here the genes that have a p-value of p <= 0.05.
The y-axis position represents the -log p-value: a higher value indicates that the gene is more significant. The x-axis position shows the log-fold-change for the gene between the engineered and wild-type samples. Genes on the right-hand side of the plot increase in expression in the engineered sample. Genes on the left-hand side decrease in expression in the engineered sample.
Treatment1-Day4 vs. Control-Day4
Treatment2-Day4 vs. Control-Day4
Treatment2-Day4 vs. Control-Day4
Treatment2-Day4 vs. Control-Day4
Treatment1-Day7 vs. Control-Day7
Treatment2-Day7 vs. Control-Day7
Treatment3-Day7 vs. Control-Day7
Treatment4-Day7 vs. Control-Day7
Treatment1-Day14 vs. Control-Day14
Treatment2-Day14 vs. Control-Day14
Treatment3-Day14 vs. Control-Day14
Treatment4-Day14 vs. Control-Day14
Full table
The full list of differentially expressed genes can be found in the tables below. Click the “Download” button to view a version of the data in Excel.
| description | |
|---|---|
| symbol | The locus ID of the gene. |
| statistic | The test statistic for this gene. This statistic is an intermediate value used to calculate the p-value. |
| baseMean | The mean expression value across all samples in the analysis. |
| log2FC | The log2-fold-change of gene expression between the engineered strain and wild-type control |
| padj | The p-value for this gene, corrected for multiple testing. |
Treatment1-Day4 vs. Control-Day4
There are 1 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.
Treatment2-Day4 vs. Control-Day4
There are 9 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.
Treatment2-Day4 vs. Control-Day4
There are 9 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.
Treatment2-Day4 vs. Control-Day4
There are 9 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.
Treatment1-Day7 vs. Control-Day7
There are 0 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.
Treatment2-Day7 vs. Control-Day7
There are 12 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.
Treatment3-Day7 vs. Control-Day7
There are 8 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.
Treatment4-Day7 vs. Control-Day7
There are 128 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.
Treatment1-Day14 vs. Control-Day14
There are 0 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.
Treatment2-Day14 vs. Control-Day14
There are 0 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.
Treatment3-Day14 vs. Control-Day14
There are 7 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.
Treatment4-Day14 vs. Control-Day14
There are 11 differentially expressed genes in this experiment at FDR-adjusted p-value of p < 0.05.
Barplots
Below are barplots of the normalized read counts for each locus ID within a CDK cluster.
ORF1_MeT_LM541
GN003446.00_002768
ORF2_ETaG_LM565
GN003446.00_003104
ORF3_Unk_LM541
GN003446.00_002654
ORF4_VOC_LM565
GN003446.00_002608
ORF5_SDR_LM565
GN003446.00_002540
ORF6_hydrolase_LM565
GN003446.00_002439
ORF7_P450_LM565
GN003446.00_002333
ORF8_P450_LM565
GN003446.00_002184
ORF9_PKS_LM565
GN003446.00_001767
ORF9_PKS_LM565-KO
GN003446.00_001767-KO
ORF10_transport_LM565
GN003446.00_002892
ORF11_TF_LM565
GN003446.00_001668
all
Conclusions
R session info
This section includes technical details about the R code used to produce this analysis. Most readers can safely ignore it.
## setting value
## version R version 3.6.0 (2019-04-26)
## os macOS 10.15.5
## system x86_64, darwin17.7.0
## ui unknown
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz America/New_York
## date 2020-07-06| package | ondiskversion | loadedversion | path | loadedpath | attached | is_base | date | source | md5ok | library | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| acepack | acepack | 1.4.1 | 1.4.1 | /usr/local/lib/R/3.6/site-library/acepack | /usr/local/lib/R/3.6/site-library/acepack | FALSE | FALSE | 2016-10-29 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| annotate | annotate | 1.62.0 | 1.62.0 | /usr/local/lib/R/3.6/site-library/annotate | /usr/local/lib/R/3.6/site-library/annotate | TRUE | FALSE | 2019-05-02 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| AnnotationDbi | AnnotationDbi | 1.46.1 | 1.46.1 | /usr/local/lib/R/3.6/site-library/AnnotationDbi | /usr/local/lib/R/3.6/site-library/AnnotationDbi | TRUE | FALSE | 2019-08-20 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| assertthat | assertthat | 0.2.1 | 0.2.1 | /usr/local/lib/R/3.6/site-library/assertthat | /usr/local/lib/R/3.6/site-library/assertthat | FALSE | FALSE | 2019-03-21 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| backports | backports | 1.1.6 | 1.1.6 | /usr/local/lib/R/3.6/site-library/backports | /usr/local/lib/R/3.6/site-library/backports | FALSE | FALSE | 2020-04-05 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| base64enc | base64enc | 0.1.3 | 0.1-3 | /usr/local/lib/R/3.6/site-library/base64enc | /usr/local/lib/R/3.6/site-library/base64enc | FALSE | FALSE | 2015-07-28 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| Biobase | Biobase | 2.44.0 | 2.44.0 | /usr/local/lib/R/3.6/site-library/Biobase | /usr/local/lib/R/3.6/site-library/Biobase | TRUE | FALSE | 2019-05-02 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| BiocGenerics | BiocGenerics | 0.30.0 | 0.30.0 | /usr/local/lib/R/3.6/site-library/BiocGenerics | /usr/local/lib/R/3.6/site-library/BiocGenerics | TRUE | FALSE | 2019-05-02 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| BiocParallel | BiocParallel | 1.18.1 | 1.18.1 | /usr/local/lib/R/3.6/site-library/BiocParallel | /usr/local/lib/R/3.6/site-library/BiocParallel | TRUE | FALSE | 2019-08-06 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| biomaRt | biomaRt | 2.40.5 | 2.40.5 | /usr/local/lib/R/3.6/site-library/biomaRt | /usr/local/lib/R/3.6/site-library/biomaRt | TRUE | FALSE | 2019-10-01 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| bit | bit | 1.1.15.2 | 1.1-15.2 | /usr/local/lib/R/3.6/site-library/bit | /usr/local/lib/R/3.6/site-library/bit | FALSE | FALSE | 2020-02-10 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| bit64 | bit64 | 0.9.7 | 0.9-7 | /usr/local/lib/R/3.6/site-library/bit64 | /usr/local/lib/R/3.6/site-library/bit64 | FALSE | FALSE | 2017-05-08 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| bitops | bitops | 1.0.6 | 1.0-6 | /usr/local/lib/R/3.6/site-library/bitops | /usr/local/lib/R/3.6/site-library/bitops | FALSE | FALSE | 2013-08-17 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| blob | blob | 1.2.1 | 1.2.1 | /usr/local/lib/R/3.6/site-library/blob | /usr/local/lib/R/3.6/site-library/blob | FALSE | FALSE | 2020-01-20 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| bvenn | bvenn | 0.1 | 0.1 | /usr/local/lib/R/3.6/site-library/bvenn | /usr/local/lib/R/3.6/site-library/bvenn | TRUE | FALSE | 2012-08-09 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| Cairo | Cairo | 1.5.12 | 1.5-12 | /usr/local/lib/R/3.6/site-library/Cairo | /usr/local/lib/R/3.6/site-library/Cairo | FALSE | FALSE | 2020-04-11 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| callr | callr | 3.4.3 | 3.4.3 | /usr/local/lib/R/3.6/site-library/callr | /usr/local/lib/R/3.6/site-library/callr | FALSE | FALSE | 2020-03-28 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| cellranger | cellranger | 1.1.0 | 1.1.0 | /usr/local/lib/R/3.6/site-library/cellranger | /usr/local/lib/R/3.6/site-library/cellranger | FALSE | FALSE | 2016-07-27 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| checkmate | checkmate | 2.0.0 | 2.0.0 | /usr/local/lib/R/3.6/site-library/checkmate | /usr/local/lib/R/3.6/site-library/checkmate | FALSE | FALSE | 2020-02-06 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| cli | cli | 2.0.2 | 2.0.2 | /usr/local/lib/R/3.6/site-library/cli | /usr/local/lib/R/3.6/site-library/cli | FALSE | FALSE | 2020-02-28 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| cluster | cluster | 2.1.0 | 2.1.0 | /usr/local/Cellar/r/3.6.0_3/lib/R/library/cluster | /usr/local/Cellar/r/3.6.0_3/lib/R/library/cluster | FALSE | FALSE | 2019-06-19 | CRAN (R 3.6.0) | NA | /usr/local/Cellar/r/3.6.0_3/lib/R/library |
| colorspace | colorspace | 1.4.1 | 1.4-1 | /usr/local/lib/R/3.6/site-library/colorspace | /usr/local/lib/R/3.6/site-library/colorspace | FALSE | FALSE | 2019-03-18 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| crayon | crayon | 1.3.4 | 1.3.4 | /usr/local/lib/R/3.6/site-library/crayon | /usr/local/lib/R/3.6/site-library/crayon | FALSE | FALSE | 2017-09-16 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| crosstalk | crosstalk | 1.1.0.1 | 1.1.0.1 | /usr/local/lib/R/3.6/site-library/crosstalk | /usr/local/lib/R/3.6/site-library/crosstalk | FALSE | FALSE | 2020-03-13 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| data.table | data.table | 1.12.8 | 1.12.8 | /usr/local/lib/R/3.6/site-library/data.table | /usr/local/lib/R/3.6/site-library/data.table | FALSE | FALSE | 2019-12-09 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| DBI | DBI | 1.1.0 | 1.1.0 | /usr/local/lib/R/3.6/site-library/DBI | /usr/local/lib/R/3.6/site-library/DBI | FALSE | FALSE | 2019-12-15 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| DelayedArray | DelayedArray | 0.10.0 | 0.10.0 | /usr/local/lib/R/3.6/site-library/DelayedArray | /usr/local/lib/R/3.6/site-library/DelayedArray | TRUE | FALSE | 2019-05-02 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| desc | desc | 1.2.0 | 1.2.0 | /usr/local/lib/R/3.6/site-library/desc | /usr/local/lib/R/3.6/site-library/desc | FALSE | FALSE | 2018-05-01 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| DESeq2 | DESeq2 | 1.24.0 | 1.24.0 | /usr/local/lib/R/3.6/site-library/DESeq2 | /usr/local/lib/R/3.6/site-library/DESeq2 | TRUE | FALSE | 2019-05-02 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| devtools | devtools | 2.3.0 | 2.3.0 | /usr/local/lib/R/3.6/site-library/devtools | /usr/local/lib/R/3.6/site-library/devtools | FALSE | FALSE | 2020-04-10 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| digest | digest | 0.6.25 | 0.6.25 | /usr/local/lib/R/3.6/site-library/digest | /usr/local/lib/R/3.6/site-library/digest | FALSE | FALSE | 2020-02-23 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| dplyr | dplyr | 0.8.5 | 0.8.5 | /usr/local/lib/R/3.6/site-library/dplyr | /usr/local/lib/R/3.6/site-library/dplyr | TRUE | FALSE | 2020-03-07 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| DT | DT | 0.13 | 0.13 | /usr/local/lib/R/3.6/site-library/DT | /usr/local/lib/R/3.6/site-library/DT | TRUE | FALSE | 2020-03-23 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| ellipsis | ellipsis | 0.3.0 | 0.3.0 | /usr/local/lib/R/3.6/site-library/ellipsis | /usr/local/lib/R/3.6/site-library/ellipsis | FALSE | FALSE | 2019-09-20 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| evaluate | evaluate | 0.14 | 0.14 | /usr/local/lib/R/3.6/site-library/evaluate | /usr/local/lib/R/3.6/site-library/evaluate | FALSE | FALSE | 2019-05-28 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| fansi | fansi | 0.4.1 | 0.4.1 | /usr/local/lib/R/3.6/site-library/fansi | /usr/local/lib/R/3.6/site-library/fansi | FALSE | FALSE | 2020-01-08 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| farver | farver | 2.0.3 | 2.0.3 | /usr/local/lib/R/3.6/site-library/farver | /usr/local/lib/R/3.6/site-library/farver | FALSE | FALSE | 2020-01-16 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| fastmatch | fastmatch | 1.1.0 | 1.1-0 | /usr/local/lib/R/3.6/site-library/fastmatch | /usr/local/lib/R/3.6/site-library/fastmatch | FALSE | FALSE | 2017-01-28 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| fgsea | fgsea | 1.10.1 | 1.10.1 | /usr/local/lib/R/3.6/site-library/fgsea | /usr/local/lib/R/3.6/site-library/fgsea | TRUE | FALSE | 2019-08-21 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| foreign | foreign | 0.8.76 | 0.8-76 | /usr/local/Cellar/r/3.6.0_3/lib/R/library/foreign | /usr/local/Cellar/r/3.6.0_3/lib/R/library/foreign | FALSE | FALSE | 2020-03-03 | CRAN (R 3.6.0) | NA | /usr/local/Cellar/r/3.6.0_3/lib/R/library |
| Formula | Formula | 1.2.3 | 1.2-3 | /usr/local/lib/R/3.6/site-library/Formula | /usr/local/lib/R/3.6/site-library/Formula | FALSE | FALSE | 2018-05-03 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| fs | fs | 1.4.1 | 1.4.1 | /usr/local/lib/R/3.6/site-library/fs | /usr/local/lib/R/3.6/site-library/fs | FALSE | FALSE | 2020-04-04 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| genefilter | genefilter | 1.66.0 | 1.66.0 | /usr/local/lib/R/3.6/site-library/genefilter | /usr/local/lib/R/3.6/site-library/genefilter | FALSE | FALSE | 2019-05-02 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| geneplotter | geneplotter | 1.62.0 | 1.62.0 | /usr/local/lib/R/3.6/site-library/geneplotter | /usr/local/lib/R/3.6/site-library/geneplotter | FALSE | FALSE | 2019-05-02 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| GenomeInfoDb | GenomeInfoDb | 1.20.0 | 1.20.0 | /usr/local/lib/R/3.6/site-library/GenomeInfoDb | /usr/local/lib/R/3.6/site-library/GenomeInfoDb | TRUE | FALSE | 2019-05-02 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| GenomeInfoDbData | GenomeInfoDbData | 1.2.1 | 1.2.1 | /usr/local/lib/R/3.6/site-library/GenomeInfoDbData | /usr/local/lib/R/3.6/site-library/GenomeInfoDbData | FALSE | FALSE | 2019-07-01 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| GenomicRanges | GenomicRanges | 1.36.1 | 1.36.1 | /usr/local/lib/R/3.6/site-library/GenomicRanges | /usr/local/lib/R/3.6/site-library/GenomicRanges | TRUE | FALSE | 2019-09-06 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| ggplot2 | ggplot2 | 3.3.0 | 3.3.0 | /usr/local/lib/R/3.6/site-library/ggplot2 | /usr/local/lib/R/3.6/site-library/ggplot2 | TRUE | FALSE | 2020-03-05 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| glue | glue | 1.4.0 | 1.4.0 | /usr/local/lib/R/3.6/site-library/glue | /usr/local/lib/R/3.6/site-library/glue | FALSE | FALSE | 2020-04-03 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| graph | graph | 1.62.0 | 1.62.0 | /usr/local/lib/R/3.6/site-library/graph | /usr/local/lib/R/3.6/site-library/graph | TRUE | FALSE | 2019-05-02 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| gridExtra | gridExtra | 2.3 | 2.3 | /usr/local/lib/R/3.6/site-library/gridExtra | /usr/local/lib/R/3.6/site-library/gridExtra | FALSE | FALSE | 2017-09-09 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| GSEABase | GSEABase | 1.46.0 | 1.46.0 | /usr/local/lib/R/3.6/site-library/GSEABase | /usr/local/lib/R/3.6/site-library/GSEABase | TRUE | FALSE | 2019-05-02 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| gtable | gtable | 0.3.0 | 0.3.0 | /usr/local/lib/R/3.6/site-library/gtable | /usr/local/lib/R/3.6/site-library/gtable | FALSE | FALSE | 2019-03-25 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| Hmisc | Hmisc | 4.4.0 | 4.4-0 | /usr/local/lib/R/3.6/site-library/Hmisc | /usr/local/lib/R/3.6/site-library/Hmisc | FALSE | FALSE | 2020-03-23 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| hms | hms | 0.5.3 | 0.5.3 | /usr/local/lib/R/3.6/site-library/hms | /usr/local/lib/R/3.6/site-library/hms | FALSE | FALSE | 2020-01-08 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| htmlTable | htmlTable | 1.13.3 | 1.13.3 | /usr/local/lib/R/3.6/site-library/htmlTable | /usr/local/lib/R/3.6/site-library/htmlTable | FALSE | FALSE | 2019-12-04 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| htmltools | htmltools | 0.4.0 | 0.4.0 | /usr/local/lib/R/3.6/site-library/htmltools | /usr/local/lib/R/3.6/site-library/htmltools | FALSE | FALSE | 2019-10-04 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| htmlwidgets | htmlwidgets | 1.5.1 | 1.5.1 | /usr/local/lib/R/3.6/site-library/htmlwidgets | /usr/local/lib/R/3.6/site-library/htmlwidgets | FALSE | FALSE | 2019-10-08 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| httr | httr | 1.4.1 | 1.4.1 | /usr/local/lib/R/3.6/site-library/httr | /usr/local/lib/R/3.6/site-library/httr | FALSE | FALSE | 2019-08-05 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| IRanges | IRanges | 2.18.3 | 2.18.3 | /usr/local/lib/R/3.6/site-library/IRanges | /usr/local/lib/R/3.6/site-library/IRanges | TRUE | FALSE | 2019-09-24 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| jpeg | jpeg | 0.1.8.1 | 0.1-8.1 | /usr/local/lib/R/3.6/site-library/jpeg | /usr/local/lib/R/3.6/site-library/jpeg | FALSE | FALSE | 2019-10-24 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| jsonlite | jsonlite | 1.6.1 | 1.6.1 | /usr/local/lib/R/3.6/site-library/jsonlite | /usr/local/lib/R/3.6/site-library/jsonlite | FALSE | FALSE | 2020-02-02 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| knitr | knitr | 1.28 | 1.28 | /usr/local/lib/R/3.6/site-library/knitr | /usr/local/lib/R/3.6/site-library/knitr | FALSE | FALSE | 2020-02-06 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| labeling | labeling | 0.3 | 0.3 | /usr/local/lib/R/3.6/site-library/labeling | /usr/local/lib/R/3.6/site-library/labeling | FALSE | FALSE | 2014-08-23 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| lattice | lattice | 0.20.41 | 0.20-41 | /usr/local/Cellar/r/3.6.0_3/lib/R/library/lattice | /usr/local/Cellar/r/3.6.0_3/lib/R/library/lattice | FALSE | FALSE | 2020-04-02 | CRAN (R 3.6.0) | NA | /usr/local/Cellar/r/3.6.0_3/lib/R/library |
| latticeExtra | latticeExtra | 0.6.29 | 0.6-29 | /usr/local/lib/R/3.6/site-library/latticeExtra | /usr/local/lib/R/3.6/site-library/latticeExtra | FALSE | FALSE | 2019-12-19 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| lazyeval | lazyeval | 0.2.2 | 0.2.2 | /usr/local/lib/R/3.6/site-library/lazyeval | /usr/local/lib/R/3.6/site-library/lazyeval | FALSE | FALSE | 2019-03-15 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| lifecycle | lifecycle | 0.2.0 | 0.2.0 | /usr/local/lib/R/3.6/site-library/lifecycle | /usr/local/lib/R/3.6/site-library/lifecycle | FALSE | FALSE | 2020-03-06 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| locfit | locfit | 1.5.9.4 | 1.5-9.4 | /usr/local/lib/R/3.6/site-library/locfit | /usr/local/lib/R/3.6/site-library/locfit | FALSE | FALSE | 2020-03-25 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| magrittr | magrittr | 1.5 | 1.5 | /usr/local/lib/R/3.6/site-library/magrittr | /usr/local/lib/R/3.6/site-library/magrittr | TRUE | FALSE | 2014-11-22 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| Matrix | Matrix | 1.2.18 | 1.2-18 | /usr/local/Cellar/r/3.6.0_3/lib/R/library/Matrix | /usr/local/Cellar/r/3.6.0_3/lib/R/library/Matrix | FALSE | FALSE | 2019-11-27 | CRAN (R 3.6.0) | NA | /usr/local/Cellar/r/3.6.0_3/lib/R/library |
| matrixStats | matrixStats | 0.56.0 | 0.56.0 | /usr/local/lib/R/3.6/site-library/matrixStats | /usr/local/lib/R/3.6/site-library/matrixStats | TRUE | FALSE | 2020-03-13 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| memoise | memoise | 1.1.0 | 1.1.0 | /usr/local/lib/R/3.6/site-library/memoise | /usr/local/lib/R/3.6/site-library/memoise | FALSE | FALSE | 2017-04-21 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| munsell | munsell | 0.5.0 | 0.5.0 | /usr/local/lib/R/3.6/site-library/munsell | /usr/local/lib/R/3.6/site-library/munsell | FALSE | FALSE | 2018-06-12 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| network | network | 1.16.0 | 1.16.0 | /usr/local/lib/R/3.6/site-library/network | /usr/local/lib/R/3.6/site-library/network | TRUE | FALSE | 2019-12-01 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| nnet | nnet | 7.3.13 | 7.3-13 | /usr/local/Cellar/r/3.6.0_3/lib/R/library/nnet | /usr/local/Cellar/r/3.6.0_3/lib/R/library/nnet | FALSE | FALSE | 2020-02-25 | CRAN (R 3.6.0) | NA | /usr/local/Cellar/r/3.6.0_3/lib/R/library |
| pander | pander | 0.6.3 | 0.6.3 | /usr/local/lib/R/3.6/site-library/pander | /usr/local/lib/R/3.6/site-library/pander | TRUE | FALSE | 2018-11-06 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| pheatmap | pheatmap | 1.0.12 | 1.0.12 | /usr/local/lib/R/3.6/site-library/pheatmap | /usr/local/lib/R/3.6/site-library/pheatmap | TRUE | FALSE | 2019-01-04 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| pillar | pillar | 1.4.4 | 1.4.4 | /usr/local/lib/R/3.6/site-library/pillar | /usr/local/lib/R/3.6/site-library/pillar | FALSE | FALSE | 2020-05-05 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| pkgbuild | pkgbuild | 1.0.8 | 1.0.8 | /usr/local/lib/R/3.6/site-library/pkgbuild | /usr/local/lib/R/3.6/site-library/pkgbuild | FALSE | FALSE | 2020-05-07 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| pkgconfig | pkgconfig | 2.0.3 | 2.0.3 | /usr/local/lib/R/3.6/site-library/pkgconfig | /usr/local/lib/R/3.6/site-library/pkgconfig | FALSE | FALSE | 2019-09-22 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| pkgload | pkgload | 1.0.2 | 1.0.2 | /usr/local/lib/R/3.6/site-library/pkgload | /usr/local/lib/R/3.6/site-library/pkgload | FALSE | FALSE | 2018-10-29 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| plotly | plotly | 4.9.2.1 | 4.9.2.1 | /usr/local/lib/R/3.6/site-library/plotly | /usr/local/lib/R/3.6/site-library/plotly | TRUE | FALSE | 2020-04-04 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| plyr | plyr | 1.8.6 | 1.8.6 | /usr/local/lib/R/3.6/site-library/plyr | /usr/local/lib/R/3.6/site-library/plyr | TRUE | FALSE | 2020-03-03 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| png | png | 0.1.7 | 0.1-7 | /usr/local/lib/R/3.6/site-library/png | /usr/local/lib/R/3.6/site-library/png | FALSE | FALSE | 2013-12-03 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| prettyunits | prettyunits | 1.1.1 | 1.1.1 | /usr/local/lib/R/3.6/site-library/prettyunits | /usr/local/lib/R/3.6/site-library/prettyunits | FALSE | FALSE | 2020-01-24 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| processx | processx | 3.4.2 | 3.4.2 | /usr/local/lib/R/3.6/site-library/processx | /usr/local/lib/R/3.6/site-library/processx | FALSE | FALSE | 2020-02-09 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| progress | progress | 1.2.2 | 1.2.2 | /usr/local/lib/R/3.6/site-library/progress | /usr/local/lib/R/3.6/site-library/progress | FALSE | FALSE | 2019-05-16 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| ps | ps | 1.3.2 | 1.3.2 | /usr/local/lib/R/3.6/site-library/ps | /usr/local/lib/R/3.6/site-library/ps | FALSE | FALSE | 2020-02-13 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| purrr | purrr | 0.3.4 | 0.3.4 | /usr/local/lib/R/3.6/site-library/purrr | /usr/local/lib/R/3.6/site-library/purrr | FALSE | FALSE | 2020-04-17 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| R6 | R6 | 2.4.1 | 2.4.1 | /usr/local/lib/R/3.6/site-library/R6 | /usr/local/lib/R/3.6/site-library/R6 | FALSE | FALSE | 2019-11-12 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| RColorBrewer | RColorBrewer | 1.1.2 | 1.1-2 | /usr/local/lib/R/3.6/site-library/RColorBrewer | /usr/local/lib/R/3.6/site-library/RColorBrewer | FALSE | FALSE | 2014-12-07 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| Rcpp | Rcpp | 1.0.4.6 | 1.0.4.6 | /usr/local/lib/R/3.6/site-library/Rcpp | /usr/local/lib/R/3.6/site-library/Rcpp | TRUE | FALSE | 2020-04-09 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| RCurl | RCurl | 1.98.1.2 | 1.98-1.2 | /usr/local/lib/R/3.6/site-library/RCurl | /usr/local/lib/R/3.6/site-library/RCurl | FALSE | FALSE | 2020-04-18 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| readxl | readxl | 1.3.1 | 1.3.1 | /usr/local/lib/R/3.6/site-library/readxl | /usr/local/lib/R/3.6/site-library/readxl | TRUE | FALSE | 2019-03-13 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| remotes | remotes | 2.1.1 | 2.1.1 | /usr/local/lib/R/3.6/site-library/remotes | /usr/local/lib/R/3.6/site-library/remotes | FALSE | FALSE | 2020-02-15 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| reshape2 | reshape2 | 1.4.4 | 1.4.4 | /usr/local/lib/R/3.6/site-library/reshape2 | /usr/local/lib/R/3.6/site-library/reshape2 | TRUE | FALSE | 2020-04-09 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| rlang | rlang | 0.4.6 | 0.4.6 | /usr/local/lib/R/3.6/site-library/rlang | /usr/local/lib/R/3.6/site-library/rlang | FALSE | FALSE | 2020-05-02 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| rmarkdown | rmarkdown | 2.1 | 2.1 | /usr/local/lib/R/3.6/site-library/rmarkdown | /usr/local/lib/R/3.6/site-library/rmarkdown | FALSE | FALSE | 2020-01-20 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| rpart | rpart | 4.1.15 | 4.1-15 | /usr/local/Cellar/r/3.6.0_3/lib/R/library/rpart | /usr/local/Cellar/r/3.6.0_3/lib/R/library/rpart | FALSE | FALSE | 2019-04-12 | CRAN (R 3.6.0) | NA | /usr/local/Cellar/r/3.6.0_3/lib/R/library |
| rprojroot | rprojroot | 1.3.2 | 1.3-2 | /usr/local/lib/R/3.6/site-library/rprojroot | /usr/local/lib/R/3.6/site-library/rprojroot | FALSE | FALSE | 2018-01-03 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| RSQLite | RSQLite | 2.2.0 | 2.2.0 | /usr/local/lib/R/3.6/site-library/RSQLite | /usr/local/lib/R/3.6/site-library/RSQLite | FALSE | FALSE | 2020-01-07 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| rstudioapi | rstudioapi | 0.11 | 0.11 | /usr/local/lib/R/3.6/site-library/rstudioapi | /usr/local/lib/R/3.6/site-library/rstudioapi | FALSE | FALSE | 2020-02-07 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| S4Vectors | S4Vectors | 0.22.1 | 0.22.1 | /usr/local/lib/R/3.6/site-library/S4Vectors | /usr/local/lib/R/3.6/site-library/S4Vectors | TRUE | FALSE | 2019-09-09 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| scales | scales | 1.1.0 | 1.1.0 | /usr/local/lib/R/3.6/site-library/scales | /usr/local/lib/R/3.6/site-library/scales | FALSE | FALSE | 2019-11-18 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| sessioninfo | sessioninfo | 1.1.1 | 1.1.1 | /usr/local/lib/R/3.6/site-library/sessioninfo | /usr/local/lib/R/3.6/site-library/sessioninfo | FALSE | FALSE | 2018-11-05 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| stringi | stringi | 1.4.6 | 1.4.6 | /usr/local/lib/R/3.6/site-library/stringi | /usr/local/lib/R/3.6/site-library/stringi | FALSE | FALSE | 2020-02-17 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| stringr | stringr | 1.4.0 | 1.4.0 | /usr/local/lib/R/3.6/site-library/stringr | /usr/local/lib/R/3.6/site-library/stringr | FALSE | FALSE | 2019-02-10 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| SummarizedExperiment | SummarizedExperiment | 1.14.1 | 1.14.1 | /usr/local/lib/R/3.6/site-library/SummarizedExperiment | /usr/local/lib/R/3.6/site-library/SummarizedExperiment | TRUE | FALSE | 2019-07-31 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| survival | survival | 3.1.12 | 3.1-12 | /usr/local/Cellar/r/3.6.0_3/lib/R/library/survival | /usr/local/Cellar/r/3.6.0_3/lib/R/library/survival | FALSE | FALSE | 2020-04-10 | CRAN (R 3.6.0) | NA | /usr/local/Cellar/r/3.6.0_3/lib/R/library |
| testthat | testthat | 2.3.2 | 2.3.2 | /usr/local/lib/R/3.6/site-library/testthat | /usr/local/lib/R/3.6/site-library/testthat | FALSE | FALSE | 2020-03-02 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| tibble | tibble | 3.0.1 | 3.0.1 | /usr/local/lib/R/3.6/site-library/tibble | /usr/local/lib/R/3.6/site-library/tibble | FALSE | FALSE | 2020-04-20 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| tidyr | tidyr | 1.0.2 | 1.0.2 | /usr/local/lib/R/3.6/site-library/tidyr | /usr/local/lib/R/3.6/site-library/tidyr | FALSE | FALSE | 2020-01-24 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| tidyselect | tidyselect | 1.0.0 | 1.0.0 | /usr/local/lib/R/3.6/site-library/tidyselect | /usr/local/lib/R/3.6/site-library/tidyselect | FALSE | FALSE | 2020-01-27 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| usethis | usethis | 1.6.0 | 1.6.0 | /usr/local/lib/R/3.6/site-library/usethis | /usr/local/lib/R/3.6/site-library/usethis | FALSE | FALSE | 2020-04-09 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| vctrs | vctrs | 0.2.4 | 0.2.4 | /usr/local/lib/R/3.6/site-library/vctrs | /usr/local/lib/R/3.6/site-library/vctrs | FALSE | FALSE | 2020-03-10 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| viridisLite | viridisLite | 0.3.0 | 0.3.0 | /usr/local/lib/R/3.6/site-library/viridisLite | /usr/local/lib/R/3.6/site-library/viridisLite | FALSE | FALSE | 2018-02-01 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| withr | withr | 2.2.0 | 2.2.0 | /usr/local/lib/R/3.6/site-library/withr | /usr/local/lib/R/3.6/site-library/withr | FALSE | FALSE | 2020-04-20 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| xfun | xfun | 0.13 | 0.13 | /usr/local/lib/R/3.6/site-library/xfun | /usr/local/lib/R/3.6/site-library/xfun | FALSE | FALSE | 2020-04-13 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| XML | XML | 3.99.0.3 | 3.99-0.3 | /usr/local/lib/R/3.6/site-library/XML | /usr/local/lib/R/3.6/site-library/XML | TRUE | FALSE | 2020-01-20 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| xtable | xtable | 1.8.4 | 1.8-4 | /usr/local/lib/R/3.6/site-library/xtable | /usr/local/lib/R/3.6/site-library/xtable | FALSE | FALSE | 2019-04-21 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| XVector | XVector | 0.24.0 | 0.24.0 | /usr/local/lib/R/3.6/site-library/XVector | /usr/local/lib/R/3.6/site-library/XVector | FALSE | FALSE | 2019-05-02 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |
| yaml | yaml | 2.2.1 | 2.2.1 | /usr/local/lib/R/3.6/site-library/yaml | /usr/local/lib/R/3.6/site-library/yaml | FALSE | FALSE | 2020-02-01 | CRAN (R 3.6.0) | NA | /usr/local/lib/R/3.6/site-library |
| zlibbioc | zlibbioc | 1.30.0 | 1.30.0 | /usr/local/lib/R/3.6/site-library/zlibbioc | /usr/local/lib/R/3.6/site-library/zlibbioc | FALSE | FALSE | 2019-05-02 | Bioconductor | NA | /usr/local/lib/R/3.6/site-library |